Collapse subtitle with bquote in ggplot2

Question

I am trying change my subtitle to read "All Subjects as Treated at 5x10^7 TCID50" with the 7 superscript and the 50 subscript.

I was able to run the following plot, where there are spaces ("5 x 10"):

With the following code:

kmcurve1 <- ggsurvplot(km_p1p2_p2dose_fit, 
              palette = c("#202960", "#8CC63E"), 
              xlab = "Time (Months)", 
              legend.labs = c("Phase 1", "Phase 2"), 
              break.time.by = 6, 
              xlim = c(0,36), 
              conf.int = FALSE, 
              pval = TRUE, 
              pval.size = 5, 
              pval.method.size = 5, 
              pval.coord = c(30,0.9), 
              pval.method.coord = c(30,1), 
              pval.method = TRUE, 
              surv.median.line = "v", 
              risk.table = "abs_pct", 
              risk.table.col = "strata", 
              surv.plot.height = 2, 
              risk.table.height = 0.24, 
              censor.shape = "|", 
              censor.size = 5, 
              font.title = 28, 
              font.x = 14, 
              font.y = 14,
              font.tickslab = 12,
              risk.table.fontsize = 3.5)

kmcurve1$plot <- kmcurve1$plot +
  labs(title = "Overall Survival for Phase 1 and Phase 2",
       subtitle = bquote(All~Subjects~as~Treated~at~5.0~x~10^7~TCID[50]),
        caption = bquote(TCID[50]~-~Median~Tissue~Culture~Infectious~Dose)) +
        theme(#text = element_text(family = "serif"), #only run for PDF output
              plot.title = element_text(size = 20), 
              plot.subtitle = element_text(size = 16), 
              plot.caption = element_text(size = 12),
              legend.text = element_text(size = 12), 
              legend.title = element_text(size = 12), 
              legend.key.size = unit(16, "points"), 
              axis.title.x = element_text(size = 14), 
              axis.title.y = element_text(size = 14),
              axis.text.x = element_text(size = 12), 
              axis.text.y = element_text(size = 12))

kmcurve1

I have removed the study numbers to avoid having identifying information.

For the subtitle, I have also tried bquote(All~Subjects~as~Treated~at~5.0x10^7~TCID[50]), which gives me the following error message:

Error: unexpected symbol in: " labs(title = "Overall Survival for Phase 1 and Phase 2", subtitle = bquote(All~Subjects~as~Treated~at~5.0x10"

Let me know if it would be helpful to have a reprex of the KM fit to replicate the curve.

user_1855677 · Answer

The only bit of knowledge you were missing is the need to use an asterisk to separate the tokens in an expression when you do not want a space to appear between them. A token cannot begin with digit, so your expression argument should have been:

  bquote(All~Subjects~as~Treated~at~5.0*x*10^7~TCID[50])

Using xilliam's example since it has much less material extraneous to the question. And I used teh function expression since you were not substituting or accessing values from the calling environment.

library(survminer)
library(survival)

fit<- survfit(Surv(time, status) ~ sex, data = lung)
p <- ggsurvplot(fit, data = lung)

p$plot +
    labs(title = "Overall Survival for Phase 1 and Phase 2",
         subtitle = expression(
            All~Subjects~as~Treated~at~5*x*10^7~TCID[50]),
         caption = expression(
            TCID[50]~-~Median~Tissue~Culture~Infectious~Dose))

Gives:

user_5456906 · Answer

One approach to showing the subtitle without spaces around the 'x' would be to replace part of your math expression with the string '5x10'. bquote is able to combine math expressions with strings. Here is your subtitle presented in a reproducible plot.

library(survminer)
library(survival)

fit<- survfit(Surv(time, status) ~ sex, data = lung)
p <- ggsurvplot(fit, data = lung)

  p$plot +
  labs(title = "Overall Survival for Phase 1 and Phase 2",
       subtitle = bquote(All~Subjects~as~Treated~at~'5x10'^7~TCID[50]),
       caption = bquote(TCID[50]~-~Median~Tissue~Culture~Infectious~Dose))

Collapse subtitle with bquote in ggplot2

2 Answers